From b8d7d96e316a3ff5ff94ec27b0bf578d2ff3dcc6 Mon Sep 17 00:00:00 2001
From: Sage Wright <sage.wright@theiagen.com>
Date: Mon, 18 Nov 2024 15:20:33 +0000
Subject: [PATCH] reorder trimmomatic base crop stuff

---
 tasks/quality_control/read_filtering/task_trimmomatic.wdl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tasks/quality_control/read_filtering/task_trimmomatic.wdl b/tasks/quality_control/read_filtering/task_trimmomatic.wdl
index e8a246497..42f62559d 100644
--- a/tasks/quality_control/read_filtering/task_trimmomatic.wdl
+++ b/tasks/quality_control/read_filtering/task_trimmomatic.wdl
@@ -40,9 +40,9 @@ task trimmomatic_pe {
     -threads ~{cpu} \
     ~{read1} ~{read2} \
     -baseout ~{samplename}.fastq.gz \
+    "${CROPPING_VAR}" \
     SLIDINGWINDOW:~{trimmomatic_window_size}:~{trimmomatic_quality_trim_score} \
-    MINLEN:~{trimmomatic_min_length} &> ~{samplename}.trim.stats.txt \
-    "${CROPPING_VAR}"
+    MINLEN:~{trimmomatic_min_length} &> ~{samplename}.trim.stats.txt
 
   >>>
   output {